Journal PDFs are provided below only within fair use, i.e. criticism, comment, news reporting, teaching (including multiple copies for classroom use), scholarship, or research, that is not an infringement of copyright.


Reviews and books



Konrad Gras, David Fange, & Johan Elf (2024)
The Escherichia coli chromosome moves to the replisome
Nature Communications Accepted for publication


Anna Knöppel, Oscar Broström, Konrad Gras, Johan Elf, and David Fange (2023)
Regulatory elements coordinating initiation of chromosome replication to the Escherichia coli cell cycle
PNAS 120 (22) e2213795120 Access the paper

Elias Amselem, Bo Broadwater, Tora Hävermark, Magnus Johansson & Johan Elf (2023)
Real-time single-molecule 3D tracking in E. coli based on cross-entropy minimization
Nature Communications 14;1336 Access the paper

Malin Lüking, David Van der Spoel, Johan Elf, and Gareth Tribello (2023)
Can molecular dynamics be used to simulate biomolecular recognition?
Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 158, no 18. PDF

Gerrit Brandis, Jimmy Larsson, and Johan Elf (2023)
Antibiotic perseverance increases the risk of resistance development
PNAS 120 (2) e2216216120 Free access to the paper


Malin Lüking, Johan Elf, and Yaakov Levy (2022)
Conformational Change of Transcription Factors from Search to Specific Binding: A lac Repressor Case Study
J. Phys. Chem. B Access the paper

Vinodh Kandavalli, Praneeth Karempudi, Jimmy Larsson & Johan Elf (2022)
Rapid antibiotic susceptibility testing and species identification for mixed samples
Nature Communications 13 (6215). Access the paper

Emil Marklund, Guanzhong Mao, Jinwen Yuan, Spartak Zikrin, Eldar Abdurakhmanov, Sebastian Deindl, Johan Elf (2022)
Sequence specificity in DNA binding is mainly governed by association
Science 375 (6579) pp. 442-445. Free access to the paper


Jakub Wiktor, Arvid H Gynnå, Prune Leroy, Jimmy Larsson, Giovanna Coceano, Ilaria Testa, Johan Elf (2021)
RecA finds homologous DNA by reduced dimensionality search
Nature 597, pages 426–429 Access the paper

Cátia Pereira, Jimmy Larsson, Karin Hjort, Johan Elf & Dan I. Andersson (2021)
The highly dynamic nature of bacterial heteroresistance impairs its clinical detection
Communications Biology 4(521). PDF


E. Marklund, B. van Oosten, G. Mao, E. Amselem, K. Kipper, A. Sabantsev, A. Emmerich, D. Globisch, X. Zheng, L. C. Lehmann, O. Berg, M. Johansson, J. Elf, S. Deindl (2020)
DNA surface exploration and operator bypassing during target search.
Nature volume 583, pages 858–861. PDF


Daniel Camsund, Michael J. Lawson, Jimmy Larsson, Daniel Jones, Spartak Zikrin, David Fange & Johan Elf (2019)
Time-resolved imaging-based CRISPRi screening.
Nature Methods doi:10.1038/s41592-019-0629-y. PDF The dataset is publicly available in IDR. It can be found under study idr0065 and using the links, and

Q. Liao, M. Lüking, D. M. Krüger, S. Deindl, J. Elf, P. M. Kasson and S. C. L. Kamerlin (2019).
Long time-scale atomistic simulations of the structure and dynamics of transcription factor-DNA recognition.
J. Phys. Chem. B 2019, DOI: 10.1021/acs.jpcb.8b12363


Martin Linden and Johan Elf (2018)
Variational algorithms for analyzing noisy multi-state diffusion trajectories
Biophysical Journal, 115(2), 276-282 PDF

Kalle Kipper, Nadja Eremina, Emil Marklund, Sumera Tubasum, Guanzhong Mao, Laura Christina Lehmann, Johan Elf, Sebastian Deindl (2018)
Structure-guided approach to site-specific fluorophore labeling of the lac repressor LacI
PLoS ONE 13(6): e0198416 PDF

Ghosh A, Baltekin O, Waneskog M, Elkhalifa D, Hammarlof DL, Elf J, Koskiniemi S. (2018)
Contact-dependent growth inhibition induces high levels of antibiotic-tolerant persister cells in clonal bacterial populations.
EMBO J, 37(9), e98026. PDF

Ivan L. Volkov, Martin Linden, Javier Aguirre Rivera, Ka-Weng Ieong, Mikhail Metelev, Johan Elf and Magnus Johansson (2018)
tRNA tracking for direct measurements of protein synthesis kinetics in live cells.
Nature Chemical Biology, doi:10.1038/s41589-018-0063-y.PDF


Michael J Lawson, Daniel Camsund, Jimmy Larsson, Ozden Baltekin, David Fange and Johan Elf (2017)
In situ genotyping of a pooled strain library after characterizing complex phenotypes.
Molecular Systems Biology 2017 13, 947. PDF

Daniel Lawson Jones, Prune Leroy, Cecilia Unoson, David Fange, Vladimir Curic, Michael J. Lawson, Johan Elf (2017)
Kinetics of dCas9 target search in Escherichia coli.
Science 357 (6358) pp1420-1424. Equal contribution. PDF

Ozden Baltekin, Alexis Boucharin, Eva Tano, Dan I. Andersson, and Johan Elf (2017)
Antibiotic susceptibility testing in less than 30 min using direct single-cell imaging.
PNAS doi: 10.1073/pnas.1708558114 PDF

Martin Linden, Vladimir Curic, Elias Amselem & Johan Elf (2017)
Pointwise error estimates in localization microscopy.
Nature Communications 8: 15115. PDF Supplementary information supplementary data


Francisco Balzarotti, Yvan Eilers, Klaus C. Gwosch, Arvid H. Gynna, Volker Westphal, Fernando D. Stefani, Johan Elf, Stefan W. Hell (2016)
Nanometer resolution imaging and tracking of fluorescent molecules with minimal photon fluxes.
Science 10.1126/science.aak9913

Kalle Kipper, Ebba G. Lundius, Vladimir Curic, Ivana Nikic, Manfred Wiessler, Edward A. Lemke, and Johan Elf (2016)
Application of Noncanonical Amino Acids for Protein Labeling in a Genomically Recoded Escherichia coli.
ACS Synthetic Biology 10.1021/acssynbio.6b00138 PDF

Johan Elf (2016)
Hypothesis: Homologous Recombination Depends on Parallel Search.
Cell Systems 3, 325-327 PDF

Johan Elf (2016)
Staying Clear of the Dragons.
Cell Systems 2, 219-220 PDF

Sanna Koskiniemi and Johan Elf (2016)
Arming the Neighborhood.
Dev. Cell 39, 5-6 PDF

Otto G Berg, Anel Mahmutovic, Emil Marklund and Johan Elf (2016)
The helical structure of DNA facilitates binding.
J. Phys. A: Math. Theor. 166, 729-739 PDF

Mats Wallden, David Fange, Ebba Gregorsson Lundius, Ozden Baltekin and Johan Elf (2016)
The Synchronization of Replication and Division Cycles in Individual E. coli Cells.
Cell 49 (2016) 364002 (17pp) PDF get data

Martin Linden, Vladimir Curic, Alexis Boucharin, David Fange and Johan Elf (2016)
Simulated single molecule microscopy with SMeagol.
Bioinformatics doi: 10.1093/bioinformatics/btw109 PDF


Ahmad Paintdakhi, Bradley Parry, Manuel Campos, Irnov Irnov, Johan Elf, Ivan Surovtsev, Christine Jacobs-Wagner (2015)
Oufti: an integrated software package for high-accuracy, high-throughput quantitative microscopy analysis.
Mol. Micro. DOI: 10.1111/mmi.13264 PDF

Sajith Kecheril Sadanandan, Ozden Baltekin, Klas E. G. Magnusson, Alexis Boucharin, Petter Ranefall, Joakim Jalden, Johan Elf, Carolina Wahlby (2015)
Segmentation and Track-analysis in Time-lapse Imaging of Bacteria.
IEEE DOI 10.1109/JSTSP.2015.2491304 PDF

Anel Mahmutovic, Otto G Berg and Johan Elf (2015)
What matters for lac repressor search in vivo - Sliding, Hopping, Intersegment Transfer, Crowding on DNA or Recognition?
Nucleic Acid Research 43(7):3454-64 PDF


Arash Sanamrad, Fredrik Persson, Ebba G. Lundius, David Fange, Arvid H. Gynna and Johan Elf (2014)
Single-particle tracking reveals that free ribosomal subunits are not excluded from the Escherichia coli nucleoid.
PNAS 10.1073/pnas.1411558111 PDF

Petter Hammar, Mats Wallden, David Fange, Fredrik Persson, Ozden Baltekin, Gustaf Ullman, Prune Leroy and Johan Elf (2014)
Direct measurement of transcription factor dissociation excludes a simple operator occupancy model for gene regulation.
Nature genetics doi:10.1038/ng.2905. * Equal contribution PDF


Erik G. Marklund, Anel Mahmutovic, Otto G. Berg, Petter Hammar, David van der Spoel, David Fange, and Johan Elf (2013)
Transcription-factor binding and sliding on DNA studied using micro- and macroscopic models-
PNAS; 110(49): 19796-19801. PDF

Andreas Grönlund, Per Lötstedt & Johan Elf (2013)
Transcription factor binding kinetics constrain noise suppression via negative feedback.
Nature Communications 4, 1864. PDF

Fredrik Persson, Martin Linden, Cecilia Unoson and Johan Elf (2013)
Extracting intracellular diffusive states and transition rates from single molecule tracking data.
Nature Methods 10, 265-269. PDF


David Fange, Anel Mahmutovic, Otto Berg and Johan Elf (2012)
Lost in presumption: stochastic reactions in spatial models.
Nature Methods, Vol. 9 no. 12 pp. 1163-1166. PDF

David Fange, Anel Mahmutovic and Johan Elf (2012)
MesoRD 1.0: Stochastic reaction-diffusion simulations in the microscopic limit.
Bioinformatics doi:10.1093/bioinformatics/bts584. PDF

Petter Hammar, Prune Leroy, Anel Mahmutovic, Erik G. Marklund, Otto G. Berg, Johan Elf (2012)
The lac repressor displays facilitated diffusion in living cells.
Science 22 June 2012: Vol. 336 no. 6088 pp. 1595-1598. PDF

G. Ullman, M. Wallden, E. G. Marklund, A. Mahmutovic, I. Razinkov, J. Elf (2012)
Hi-throughput gene expression analysis at the level of single proteins using a microfluidic turbidostat and automated cell tracking.
Philosophical Transactions B. PDF

Viktoriya Shyp, Stoyan Tankov, Andrey Ermakov, Pavel Kudrin, Brian P English, Måns Ehrenberg, Tanel Tenson, Johan Elf & Vasili Hauryliuk1 (2012)
Positive allosteric feedback regulation of the stringent response enzyme RelA by its product.
EMBO reports 20 July, 2012. PDF


Anton Kuzmenko, Stoyan Tankov, Brian P. English, Ivan Tarassov, Tanel Tenson, Piotr Kamenski, Johan Elf & Vasili Hauryliuk (2011)
Single molecule tracking fluorescence microscopy in mitochondria reveals highly dynamic but confined movement of Tom40.
Sci Rep. 2011; 1: 195. PDF

Andreas Grönlund, Per Lötstedt & Johan Elf (2011)
Delay induced anomalous fluctuations in intracellular regulation.
Nature Communications 2011 Aug 9;2:419. PDF

Brian English, Vasili Hauryliuk, Arash Sanamrad, Stoyan Tankov, Nynke Dekker & Johan Elf (2011)
Single Molecule Investigations of the Stringent Response Machinery in Living Bacterial Cells.
PNAS 108(31):E365-73. PDF

Mats Wallden & Johan Elf (2011)
Studying Transcriptional Interactions in Single Cells at Sufficinet Resolution.
Current Opinion in Biotechnology 22:81-6.PDF


David Fange, Otto G. Berg, Paul Sjöberg & Johan Elf (2010)
Stochastic reaction-diffusion kinetics in the microscopic limit.
PNAS 107:19820-5. PDF

Fender A, Elf J, Hampel K, Zimmermann B & Wagner EG (2010)
RNAs actively cycle on the Sm-like protein Hfq.
Genes & Development 24:2621-6. PDF

Andreas Grönlund, Per Lötstedt, Johan Elf (2010)
The costs and constraints from time-delayed feed-back in small gene regulatory motifs.
PNAS 107:8171-8176. PDF


Gene-Wei Li, Otto G. Berg, Johan Elf (2009)
Effects of macromolecular crowding and DNA looping on gene regulation kinetics.
Nature Physics 5, 294 - 297. PDF

Gene-Wei Li, Johan Elf (2009)
Single molecule approaches to transcription factor kinetics in living cells.
FEBS Letters 583: 3979-3983. PDF

Sjöberg P, Lötstedt P and Elf J (2009)
Fokker-Planck approximation of the master equation in molecular biology.
Computing and Visualization in Science 12:37-50. PDF


Johan Elf, Gene-Wei Li, and X. Sunney Xie (2007)
Probing Transctiption Factor Dynamics at the Single Molecule Level a Living Cell-
Science 316(5828): 1191-1194. PDF


Elf J, Nilsson K, Tenson T amd Ehrenberg M. (2006)
Bi-stable bacterial growth rate in response to antibiotics with low membrane permeability.
Physical Review letters 2006 Dec 22;97(25):258104.

Fange D and Elf J (2006)
Noise induced Min phenotypes in E. coli.
PLoS computational biology Jun 30;2(6):e80. PDF


Sörensen MA, Elf J, Bouakaz E, Tenson T, Sanyal S, Björk GR, and Ehrenberg M (2005)
Over expression of a tRNA-Leu isoacceptor changes charging pattern of leucine tRNAs and reveals new codon reading.
J Mol Biol 354, 16-24. PDF

Elf J and Ehrenberg M (2005)
What makes ribosome mediated transcriptional attenuation sensitive?
PLoS Computational Biology 1(1): e2. PDF

Hattne J, Fange D, and Elf J (2005)
Stochastic reaction-diffusion simulation with MesoRD.
Bioinformatics Vol.21 no.12, pages 2923-2924. PDF

Lindsley D, Bonthuis P, Gallant J, Tofoleanu T, Elf J and Ehrenberg M (2005)
Ribosome By-passing At Serine Codons as a Test of the Model of Selective tRNA Charging.
EMBO reports 6:147-150. PDF

Dittmar K, Sörensen M, Elf J, Ehrenberg M, Pan T, (2005)
Selective charging of tRNA isoacceptors during amino acid starvation.
EMBO reports 6:151-157. PDF

Elf, J and Ehrenberg, M (2005)
Near-critical behavior of aminoacyl-tRNA pools in E. coli at rate limiting supply of amino acids.
Biophys. J 88:132-46. PDF


Elf, J and Ehrenberg, M (2004)
Spontaneous separation of bi-stable biochemical systems into spatial domains of opposite phases.
Systems Biology Vol.1, No.2, Dec. PDF Supplementary material

Elf, J (2004)
Intracellular Flows and Fluctuations
PhD Thesis, ISBN 91-554-5988-9


Elf, J and Ehrenberg, M (2003)
Fast evaluation of fluctuations in biochemical networks with the linear noise approximation.
Genome Research 13:2475-2484. PDF

Elf, J, Nilsson, D, Tenson, T and Ehrenberg, M. (2003).
Selective charging of tRNA isoacceptors explains patterns of codon usage.
Science 300: 1718-1722. PDF

Pedersen, K., Zavialov, A., Pavlov, M., Elf, J., Gerdes, K. and Ehrenberg, M. (2003).
The bacterial toxin RelE displays codon specific cleavage of mRNAs in the ribosomal A-site.
Cell Volume 112, Issue 1, 131-140. PDF

Elf J., Paulsson J., Berg O. & Ehrenberg M.(2003)
Near-critical phenomena in intracellular metabolite pools.
Biophysical Journal 84:154-170. PDF

Elf, J, Doncic, A & Ehrenberg, M (2003)
Mesoscopic reaction-diffusion in intracellular signaling.
Proceedings of the SPIE Volume 5110, pp. 114-124. PDF

Elf, J, Lötstedt, P, and Sjöberg, P (2003).
Problems of high dimension in molecular biology.
Proceedings of the 17th GAMM-Seminar pp 1-10. PDF


Elf, J., Berg, O.G. & Ehrenberg, M. (2001)
Comparison of repressor and transcriptional attenuator systems for control of amino acid biosynthetic operons.
J. Mol. Biol, 313(5):941-954. PDF

Elf J, Fried G, Lilja L, Meister B, Bark C. (2000)
Differential sorting of SNAP-25a and SNAP-25b proteins in neuroblastoma cells.
Eur J Cell Biol.79:781-9.